title: Towards a unified paradigm for sequence-based identification of fungi.
abstract: The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database (http://unite.ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third-party annotation effort. We introduce the term 'species hypothesis' (SH) for the taxa discovered in clustering on different similarity thresholds (97-99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web-based sequence management system in UNITE.
authors.affiliation: Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia; Natural History Museum, University of Tartu, Vanemuise 46, Tartu, 51014, Estonia.
authors.forename: Urmas
authors.initials: U
authors.lastname: Kõljalg
authors.forename: R Henrik
authors.initials: RH
authors.lastname: Nilsson
authors.forename: Kessy
authors.initials: K
authors.lastname: Abarenkov
authors.forename: Leho
authors.initials: L
authors.lastname: Tedersoo
authors.forename: Andy F S
authors.initials: AF
authors.lastname: Taylor
authors.forename: Mohammad
authors.initials: M
authors.lastname: Bahram
authors.forename: Scott T
authors.initials: ST
authors.lastname: Bates
authors.forename: Thomas D
authors.initials: TD
authors.lastname: Bruns
authors.forename: Johan
authors.initials: J
authors.lastname: Bengtsson-Palme
authors.forename: Tony M
authors.initials: TM
authors.lastname: Callaghan
authors.forename: Brian
authors.initials: B
authors.lastname: Douglas
authors.forename: Tiia
authors.initials: T
authors.lastname: Drenkhan
authors.forename: Ursula
authors.initials: U
authors.lastname: Eberhardt
authors.forename: Margarita
authors.initials: M
authors.lastname: Dueñas
authors.forename: Tine
authors.initials: T
authors.lastname: Grebenc
authors.forename: Gareth W
authors.initials: GW
authors.lastname: Griffith
authors.forename: Martin
authors.initials: M
authors.lastname: Hartmann
authors.forename: Paul M
authors.initials: PM
authors.lastname: Kirk
authors.forename: Petr
authors.initials: P
authors.lastname: Kohout
authors.forename: Ellen
authors.initials: E
authors.lastname: Larsson
authors.forename: Björn D
authors.initials: BD
authors.lastname: Lindahl
authors.forename: Robert
authors.initials: R
authors.lastname: Lücking
authors.forename: María P
authors.initials: MP
authors.lastname: Martín
authors.forename: P Brandon
authors.initials: PB
authors.lastname: Matheny
authors.forename: Nhu H
authors.initials: NH
authors.lastname: Nguyen
authors.forename: Tuula
authors.initials: T
authors.lastname: Niskanen
authors.forename: Jane
authors.initials: J
authors.lastname: Oja
authors.forename: Kabir G
authors.initials: KG
authors.lastname: Peay
authors.forename: Ursula
authors.initials: U
authors.lastname: Peintner
authors.forename: Marko
authors.initials: M
authors.lastname: Peterson
authors.forename: Kadri
authors.initials: K
authors.lastname: Põldmaa
authors.forename: Lauri
authors.initials: L
authors.lastname: Saag
authors.forename: Irja
authors.initials: I
authors.lastname: Saar
authors.forename: Arthur
authors.initials: A
authors.lastname: Schüßler
authors.forename: James A
authors.initials: JA
authors.lastname: Scott
authors.forename: Carolina
authors.initials: C
authors.lastname: Senés
authors.forename: Matthew E
authors.initials: ME
authors.lastname: Smith
authors.forename: Ave
authors.initials: A
authors.lastname: Suija
authors.forename: D Lee
authors.initials: DL
authors.lastname: Taylor
authors.forename: M Teresa
authors.initials: MT
authors.lastname: Telleria
authors.forename: Michael
authors.initials: M
authors.lastname: Weiss
authors.forename: Karl-Henrik
authors.initials: KH
authors.lastname: Larsson
mesh_terms: D058893:DNA Barcoding, Taxonomic; D004271:DNA, Fungal / Q000235:genetics; D021903:DNA, Ribosomal Spacer / Q000235:genetics; D030561:Databases, Nucleic Acid; D005658:Fungi / Q000145:classification* / Q000235:genetics; D020407:Internet; D010802:Phylogeny
chemical_list: D004271:DNA, Fungal; D021903:DNA, Ribosomal Spacer
keywords: DNA barcoding; bioinformatics; ecological genomics; fungi; microbial diversity